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Perinatally-acquired HIV infection commonly causes stunting in children; how this affects bone and muscle development is unclear. We investigated differences in bone and muscle mass and muscle function between children with HIV (CWH) and uninfected children. Cross-sectional study of CWH (6–16 years) receiving antiretroviral therapy (ART) for >6 months and similar aged children testing HIV-negative at primary health clinics in Zimbabwe. From Dual-energy X-ray Absorptiometry (DXA) we calculated total-body less-head (TBLH) Bone Mineral Content (BMC) for lean mass adjusted-for-height (TBLH-BMCLBM) Z-scores, and lumbar spine (LS) Bone Mineral Apparent Density (BMAD) Z-scores. The 97 CWH were older (mean age 12.7 vs. 10.0 years) and taller (mean height 142 cm vs. 134 cm) than 77 uninfected. However, stunting (height-for-age Z-score ≤ −2) was more prevalent in CWH (35% vs. 5%, p < 0.001). Among CWH, 15% had low LS-BMAD (Z-score ≤ −2) and 13% low TBLH-BMCLBM, vs. 1% and 3% respectively in those uninfected (both p ≤ 0.02). After age, sex, height and puberty adjustment, LS-BMAD was 0.33 SDs (95%CI -0.01, 0.67; p = 0.06) lower in CWH, with no differences by HIV status in TBLH-BMCLBM, lean mass (0.11 [−0.03, 0.24], p = 0.11) or grip strength (0.05 [−0.16, 0.27], p = 0.62). However, age at ART initiation was correlated with both LS-BMAD Z-score (r = −0.33, p = 0.001) and TBLH-BMCLBM Z-score (r = −0.23, p = 0.027); for each year ART initiation was delayed a 0.13 SD reduction in LS-BMAD was seen. Size-adjusted low bone density is common in CWH. Delay in initiating ART adversely affects bone density. Findings support immediate ART initiation at HIV diagnosis. • We studied 97 children living with HIV and 77 uninfected peers aged 6 to 16 and living in Harare, Zimbabwe • A high proportion of children with HIV were stunted (height-for-age Z -score <-2) compared to those uninfected (32% vs. 5%, p <0.001) • Low lumbar spine BMAD (Z-score ≤-2) was more common among children with HIV than those uninfected, 15% vs. 1% (p =0.002) • Low lumbar spine BMAD occurred independently of stunting, i.e. stunting is not a proxy for low size-adjusted bone density • Age when starting antiretroviral therapy predicted lumbar spine BMAD; with 1 SD lower BMAD when starting after age eight • After accounting for height and pubertal stage, muscle mass and strength were similar in children with and without HIV infection [ABSTRACT FROM AUTHOR]